Chitosan, as the second most abundant biopolymer on earth, is constantly increasing attention from different fileds such as biomedicals, food, energy, and the environment. However, its application in membrane technology such as pervaporation is lacking of an effective membrane manufacture strategy to improve its separation efficiency. Herein, we use a chitosan-based membrane subjected to neutralization and crosslinking procedures in contrasting solvents—specifically, water and ethanol—to explore the impact of polymer-solvent interactions on the effective nanogaps between polymer nanofibers. Under identical conditions, the procedures conducted in water yield hydrated membranes, while those in ethanol resulted in anhydrous membranes. In hydrated membranes, strong hydrogen bonds formed between water and amine groups block nanogaps amongst polymer nanofibers, significantly impeding molecular transport. Conversely, the absence of such strong hydrogen bonds in anhydrous membrane avoided this effect. This study highlights the potential of controlling the transport of organic molecules by tuning the nanogaps within the membrane matrix. This was achieved through a novel strategy involving washing the chitosan-based membranes with pure ethanol to remove free acids, followed by direct crosslinking in a glutaraldehyde ethanol solution. This strategy was able to double the membrane selectivity despite a 25 % reduction in methanol permeance.